Overriding tw-story's parent? (Harlowe)

I'm trying to integrate Twine output into a large CMS. A problem I can't seem to work around is how Harlowe renders the tw-story passage *after* the close of the document's body tag. So even if I include it in the proper location, it seems some JS moves the content after the body tag, which means that other PHP elements render above it. I've browsed through the source on bitbucket and can't see where this location is set or how to override it.

TLDR: I need my twine stuff in the body tag, not after it. Any ideas?

Apologies if this has been asked before, it was impossible find relevant info when doing a search for the keywords "body" and "tw-story".